1
|
Li Y, Devenish C, Tosa MI, Luo M, Bell DM, Lesmeister DB, Greenfield P, Pichler M, Levi T, Yu DW. Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230123. [PMID: 38705177 DOI: 10.1098/rstb.2023.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/31/2024] [Indexed: 05/07/2024] Open
Abstract
Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These 'novel community datasets' let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km2 temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this 'sideways biodiversity modelling' method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
Collapse
Affiliation(s)
- Yuanheng Li
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
- Faculty of Biology, University of Duisburg-Essen, Essen 45141, Germany
| | - Christian Devenish
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Marie I Tosa
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Mingjie Luo
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, People's Republic of China
| | - David M Bell
- Pacific Northwest Research Station, U.S. Department of Agriculture Forest Service, Corvallis, OR 97331, USA
| | - Damon B Lesmeister
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
- Pacific Northwest Research Station, U.S. Department of Agriculture Forest Service, Corvallis, OR 97331, USA
| | - Paul Greenfield
- CSIRO Energy, Lindfield, New South Wales, Australia
- School of Biological Sciences, Macquarie University, Sydney, Australia
| | | | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Douglas W Yu
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, People's Republic of China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan 650223, People's Republic of China
| |
Collapse
|
2
|
Iwaszkiewicz-Eggebrecht E, Zizka V, Lynggaard C. Three steps towards comparability and standardization among molecular methods for characterizing insect communities. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230118. [PMID: 38705189 DOI: 10.1098/rstb.2023.0118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/10/2023] [Indexed: 05/07/2024] Open
Abstract
Molecular methods are currently some of the best-suited technologies for implementation in insect monitoring. However, the field is developing rapidly and lacks agreement on methodology or community standards. To apply DNA-based methods in large-scale monitoring, and to gain insight across commensurate data, we need easy-to-implement standards that improve data comparability. Here, we provide three recommendations for how to improve and harmonize efforts in biodiversity assessment and monitoring via metabarcoding: (i) we should adopt the use of synthetic spike-ins, which will act as positive controls and internal standards; (ii) we should consider using several markers through a multiplex polymerase chain reaction (PCR) approach; and (iii) we should commit to the publication and transparency of all protocol-associated metadata in a standardized fashion. For (i), we provide a ready-to-use recipe for synthetic cytochrome c oxidase spike-ins, which enable between-sample comparisons. For (ii), we propose two gene regions for the implementation of multiplex PCR approaches, thereby achieving a more comprehensive community description. For (iii), we offer guidelines for transparent and unified reporting of field, wet-laboratory and dry-laboratory procedures, as a key to making comparisons between studies. Together, we feel that these three advances will result in joint quality and calibration standards rather than the current laboratory-specific proof of concepts. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
Collapse
Affiliation(s)
- Ela Iwaszkiewicz-Eggebrecht
- Bioinformatics and Genetics Department, Swedish Museum of Natural History, PO Box 50007, Stockholm, 104 05, Sweden
| | - Vera Zizka
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, 53113, Germany
| | - Christina Lynggaard
- Section for Molecular Ecology & Evolution, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| |
Collapse
|
3
|
Iwaszkiewicz-Eggebrecht E, Łukasik P, Buczek M, Deng J, Hartop EA, Havnås H, Prus-Frankowska M, Ugarph CR, Viteri P, Andersson AF, Roslin T, Tack AJM, Ronquist F, Miraldo A. FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples. PLoS One 2023; 18:e0286272. [PMID: 37467453 DOI: 10.1371/journal.pone.0286272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/11/2023] [Indexed: 07/21/2023] Open
Abstract
Insects are diverse and sustain essential ecosystem functions, yet remain understudied. Recent reports about declines in insect abundance and diversity have highlighted a pressing need for comprehensive large-scale monitoring. Metabarcoding (high-throughput bulk sequencing of marker gene amplicons) offers a cost-effective and relatively fast method for characterizing insect community samples. However, the methodology applied varies greatly among studies, thus complicating the design of large-scale and repeatable monitoring schemes. Here we describe a non-destructive metabarcoding protocol that is optimized for high-throughput processing of Malaise trap samples and other bulk insect samples. The protocol details the process from obtaining bulk samples up to submitting libraries for sequencing. It is divided into four sections: 1) Laboratory workspace preparation; 2) Sample processing-decanting ethanol, measuring the wet-weight biomass and the concentration of the preservative ethanol, performing non-destructive lysis and preserving the insect material for future work; 3) DNA extraction and purification; and 4) Library preparation and sequencing. The protocol relies on readily available reagents and materials. For steps that require expensive infrastructure, such as the DNA purification robots, we suggest alternative low-cost solutions. The use of this protocol yields a comprehensive assessment of the number of species present in a given sample, their relative read abundances and the overall insect biomass. To date, we have successfully applied the protocol to more than 7000 Malaise trap samples obtained from Sweden and Madagascar. We demonstrate the data yield from the protocol using a small subset of these samples.
Collapse
Affiliation(s)
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Junchen Deng
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Emily A Hartop
- Station Linné, Färjestaden, Sweden
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Monika Prus-Frankowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | | | - Paulina Viteri
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Andreia Miraldo
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| |
Collapse
|
4
|
Paula DP, Andow DA. DNA High-Throughput Sequencing for Arthropod Gut Content Analysis to Evaluate Effectiveness and Safety of Biological Control Agents. Neotrop Entomol 2023; 52:302-332. [PMID: 36478343 DOI: 10.1007/s13744-022-01011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
The search for effective biological control agents without harmful non-target effects has been constrained by the use of impractical (field direct observation) or imprecise (cage experiments) methods. While advances in the DNA sequencing methods, more specifically the development of high-throughput sequencing (HTS), have been quickly incorporated in biodiversity surveys, they have been slow to be adopted to determine arthropod prey range, predation rate and food web structure, and critical information to evaluate the effectiveness and safety of a biological control agent candidate. The lack of knowledge on how HTS methods could be applied by ecological entomologists constitutes part of the problem, although the lack of expertise and the high cost of the analysis also are important limiting factors. In this review, we describe how the latest HTS methods of metabarcoding and Lazaro, a method to identify prey by mapping unassembled shotgun reads, can serve biological control research, showing both their power and limitations. We explain how they work to determine prey range and also how their data can be used to estimate predation rates and subsequently be translated into food webs of natural enemy and prey populations helping to elucidate their role in the community. We present a brief history of prey detection through molecular gut content analysis and also the attempts to develop a more precise formula to estimate predation rates, a problem that still remains. We focused on arthropods in agricultural ecosystems, but most of what is covered here can be applied to natural systems and non-arthropod biological control candidates as well.
Collapse
|
5
|
Chua PYS, Bourlat SJ, Ferguson C, Korlevic P, Zhao L, Ekrem T, Meier R, Lawniczak MKN. Future of DNA-based insect monitoring. Trends Genet 2023:S0168-9525(23)00038-0. [PMID: 36907721 DOI: 10.1016/j.tig.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023]
Abstract
Insects are crucial for ecosystem health but climate change and pesticide use are driving massive insect decline. To mitigate this loss, we need new and effective monitoring techniques. Over the past decade there has been a shift to DNA-based techniques. We describe key emerging techniques for sample collection. We suggest that the selection of tools should be broadened, and that DNA-based insect monitoring data need to be integrated more rapidly into policymaking. We argue that there are four key areas for advancement, including the generation of more complete DNA barcode databases to interpret molecular data, standardisation of molecular methods, scaling up of monitoring efforts, and integrating molecular tools with other technologies that allow continuous, passive monitoring based on images and/or laser imaging, detection, and ranging (LIDAR).
Collapse
Affiliation(s)
- Physilia Y S Chua
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Sarah J Bourlat
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Adenauerallee 127, 53113 Bonn, Germany
| | - Cameron Ferguson
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Petra Korlevic
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leia Zhao
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rudolf Meier
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| |
Collapse
|
6
|
Courtot É, Boisseau M, Dhorne-Pollet S, Serreau D, Gesbert A, Reigner F, Basiaga M, Kuzmina T, Lluch J, Annonay G, Kuchly C, Diekmann I, Krücken J, von Samson-Himmelstjerna G, Mach N, Sallé G. Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing. PeerJ 2023; 11:e15124. [PMID: 37070089 PMCID: PMC10105562 DOI: 10.7717/peerj.15124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 03/03/2023] [Indexed: 04/19/2023] Open
Abstract
Basic knowledge on the biology and epidemiology of equine strongylid species still needs to be improved to contribute to the design of better parasite control strategies. Nemabiome metabarcoding is a convenient tool to quantify and identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA gene, with a limited investigation of its predictive performance for cyathostomin communities. Using DNA pools of single cyathostomin worms, this study aimed to provide the first elements to compare performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. Barcode predictive abilities were compared across various mock community compositions of two, five and 11 individuals from distinct species. The amplification bias of each barcode was estimated. Results were also compared between various types of biological samples, i.e., eggs, infective larvae or adults. Bioinformatic parameters were chosen to yield the closest representation of the cyathostomin community for each barcode, underscoring the need for communities of known composition for metabarcoding purposes. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types. However, imperfect correlations were found between relative abundances from infective larvae and other life-stages for Cylicostephanus species using the ITS-2 barcode. While the results remain limited by the considered biological material, they suggest that additional improvements are needed for both the ITS-2 and COI barcodes.
Collapse
Affiliation(s)
- Élise Courtot
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
| | - Michel Boisseau
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
- Animal Health, UMR1225 IHAP, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | | | - Delphine Serreau
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
| | - Amandine Gesbert
- Animal Physiology, UEPAO, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nouzilly, France
| | - Fabrice Reigner
- Animal Physiology, UEPAO, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nouzilly, France
| | | | - Tetiana Kuzmina
- Schmalhausen Institute of Zoology NAS of Ukraine, Kyiv, Ukraine
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Slovak Republic
| | - Jérôme Lluch
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Gwenolah Annonay
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Claire Kuchly
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Irina Diekmann
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Nuria Mach
- Animal Health, UMR1225 IHAP, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Guillaume Sallé
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
| |
Collapse
|
7
|
Antil S, Abraham JS, Sripoorna S, Maurya S, Dagar J, Makhija S, Bhagat P, Gupta R, Sood U, Lal R, Toteja R. DNA barcoding, an effective tool for species identification: a review. Mol Biol Rep 2023; 50:761-775. [PMID: 36308581 DOI: 10.1007/s11033-022-08015-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/07/2022] [Indexed: 02/01/2023]
Abstract
DNA barcoding is a powerful taxonomic tool to identify and discover species. DNA barcoding utilizes one or more standardized short DNA regions for taxon identification. With the emergence of new sequencing techniques, such as Next-generation sequencing (NGS), ONT MinION nanopore sequencing, and Pac Bio sequencing, DNA barcoding has become more accurate, fast, and reliable. Rapid species identification by DNA barcodes has been used in a variety of fields, including forensic science, control of the food supply chain, and disease understanding. The Consortium for Barcode of Life (CBOL) presents various working groups to identify the universal barcode gene, such as COI in metazoans; rbcL, matK, and ITS in plants; ITS in fungi; 16S rRNA gene in bacteria and archaea, and creating a reference DNA barcode library. In this article, an attempt has been made to analyze the various proposed DNA barcode for different organisms, strengths & limitations, recent advancements in DNA barcoding, and methods to speed up the DNA barcode reference library construction. This study concludes that constructing a reference library with high species coverage would be a major step toward identifying species by DNA barcodes. This can be achieved in a short period of time by using advanced sequencing and data analysis methods.
Collapse
Affiliation(s)
- Sandeep Antil
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | | | - S Sripoorna
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Swati Maurya
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Jyoti Dagar
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Pooja Bhagat
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, New Delhi, Delhi, 110 021, India
| | - Utkarsh Sood
- The Energy and Resources Institute, IHC Complex, New Delhi, 110003, India
| | - Rup Lal
- The Energy and Resources Institute, IHC Complex, New Delhi, 110003, India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India.
| |
Collapse
|
8
|
Paula DP, Timbó RV, Togawa RC, Vogler AP, Andow DA. Quantitative prey species detection in predator guts across multiple trophic levels by mapping unassembled shotgun reads. Mol Ecol Resour 2022; 23:64-80. [DOI: 10.1111/1755-0998.13690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 06/11/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Débora P. Paula
- Embrapa Recursos Genéticos e Biotecnologia Brasília DF Brazil
| | - Renata V. Timbó
- Embrapa Recursos Genéticos e Biotecnologia Brasília DF Brazil
- Universidade de Brasília, Campus Universitário Darcy Ribeiro Brasília DF Brazil
| | | | - Alfried P. Vogler
- Imperial College London Ascot UK
- Department of Life Sciences Natural History Museum London UK
| | - David A. Andow
- Department of Entomology University of Minnesota St. Paul USA
| |
Collapse
|
9
|
van Klink R, August T, Bas Y, Bodesheim P, Bonn A, Fossøy F, Høye TT, Jongejans E, Menz MHM, Miraldo A, Roslin T, Roy HE, Ruczyński I, Schigel D, Schäffler L, Sheard JK, Svenningsen C, Tschan GF, Wäldchen J, Zizka VMA, Åström J, Bowler DE. Emerging technologies revolutionise insect ecology and monitoring. Trends Ecol Evol 2022; 37:872-885. [PMID: 35811172 DOI: 10.1016/j.tree.2022.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/26/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022]
Abstract
Insects are the most diverse group of animals on Earth, but their small size and high diversity have always made them challenging to study. Recent technological advances have the potential to revolutionise insect ecology and monitoring. We describe the state of the art of four technologies (computer vision, acoustic monitoring, radar, and molecular methods), and assess their advantages, current limitations, and future potential. We discuss how these technologies can adhere to modern standards of data curation and transparency, their implications for citizen science, and their potential for integration among different monitoring programmes and technologies. We argue that they provide unprecedented possibilities for insect ecology and monitoring, but it will be important to foster international standards via collaboration.
Collapse
Affiliation(s)
- Roel van Klink
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Martin Luther University-Halle Wittenberg, Department of Computer Science, 06099, Halle (Saale), Germany.
| | - Tom August
- UK Centre for Ecology & Hydrology, Benson Lane, Wallingford, OX10 8BB, UK
| | - Yves Bas
- Centre d'Écologie et des Sciences de la Conservation, Muséum National d'Histoire Naturelle, Paris, France; CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Paul Bodesheim
- Friedrich Schiller University Jena, Computer Vision Group, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Aletta Bonn
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburger Strasse 159, 07743, Jena, Germany
| | - Frode Fossøy
- Norwegian Institute for Nature Research, P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Toke T Høye
- Aarhus University, Department of Ecoscience and Arctic Research Centre, C.F. Møllers Allé 8, 8000, Aarhus, Denmark
| | - Eelke Jongejans
- Radboud University, Animal Ecology and Physiology, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands; Netherlands Institute of Ecology, Animal Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Myles H M Menz
- Max Planck Institute for Animal Behaviour, Department of Migration, Am Obstberg 1, 78315, Radolfzell, Germany; College of Science and Engineering, James Cook University, Townsville, Qld, Australia
| | - Andreia Miraldo
- Swedish Museum of Natural Sciences, Department of Bioinformatics and Genetics, Frescativägen 40, 114 18, Stockholm, Sweden
| | - Tomas Roslin
- Swedish University of Agricultural Sciences (SLU), Department of Ecology, Ulls väg 18B, 75651, Uppsala, Sweden
| | - Helen E Roy
- UK Centre for Ecology & Hydrology, Benson Lane, Wallingford, OX10 8BB, UK
| | - Ireneusz Ruczyński
- Mammal Research Institute, Polish Academy of Sciences, Stoczek 1, 17-230, Białowieża, Poland
| | - Dmitry Schigel
- Global Biodiversity Information Facility (GBIF), Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Livia Schäffler
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113, Bonn, Germany
| | - Julie K Sheard
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburger Strasse 159, 07743, Jena, Germany; University of Copenhagen, Centre for Macroecology, Evolution and Climate, Globe Institute, Universitetsparken 15, bld. 3, 2100, Copenhagen, Denmark
| | - Cecilie Svenningsen
- University of Copenhagen, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Georg F Tschan
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113, Bonn, Germany
| | - Jana Wäldchen
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, Hans-Knoell-Str. 10, 07745, Jena, Germany
| | - Vera M A Zizka
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113, Bonn, Germany
| | - Jens Åström
- Norwegian Institute for Nature Research, P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Diana E Bowler
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; UK Centre for Ecology & Hydrology, Benson Lane, Wallingford, OX10 8BB, UK; Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburger Strasse 159, 07743, Jena, Germany
| |
Collapse
|
10
|
Basset Y, Hajibabaei M, Wright MTG, Castillo AM, Donoso DA, Segar ST, Souto-Vilarós D, Soliman DY, Roslin T, Smith MA, Lamarre GPA, De León LF, Decaëns T, Palacios-Vargas JG, Castaño-Meneses G, Scheffrahn RH, Rivera M, Perez F, Bobadilla R, Lopez Y, Ramirez Silva JA, Cruz MM, Galván AA, Barrios H. Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera). Sci Rep 2022; 12:10762. [PMID: 35750774 PMCID: PMC9232565 DOI: 10.1038/s41598-022-14915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
The soil fauna of the tropics remains one of the least known components of the biosphere. Long-term monitoring of this fauna is hampered by the lack of taxonomic expertise and funding. These obstacles may potentially be lifted with DNA metabarcoding. To validate this approach, we studied the ants, springtails and termites of 100 paired soil samples from Barro Colorado Island, Panama. The fauna was extracted with Berlese-Tullgren funnels and then either sorted with traditional taxonomy and known, individual DNA barcodes ("traditional samples") or processed with metabarcoding ("metabarcoding samples"). We detected 49 ant, 37 springtail and 34 termite species with 3.46 million reads of the COI gene, at a mean sequence length of 233 bp. Traditional identification yielded 80, 111 and 15 species of ants, springtails and termites, respectively; 98%, 37% and 100% of these species had a Barcode Index Number (BIN) allowing for direct comparison with metabarcoding. Ants were best surveyed through traditional methods, termites were better detected by metabarcoding, and springtails were equally well detected by both techniques. Species richness was underestimated, and faunal composition was different in metabarcoding samples, mostly because 37% of ant species were not detected. The prevalence of species in metabarcoding samples increased with their abundance in traditional samples, and seasonal shifts in species prevalence and faunal composition were similar between traditional and metabarcoding samples. Probable false positive and negative species records were reasonably low (13-18% of common species). We conclude that metabarcoding of samples extracted with Berlese-Tullgren funnels appear suitable for the long-term monitoring of termites and springtails in tropical rainforests. For ants, metabarcoding schemes should be complemented by additional samples of alates from Malaise or light traps.
Collapse
Affiliation(s)
- Yves Basset
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama.
- Faculty of Science, University of South Bohemia, 370 05, Ceske Budejovice, Czech Republic.
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic.
- Maestría de Entomología, Universidad de Panamá, 080814, Panama City, Republic of Panama.
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Michael T G Wright
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Anakena M Castillo
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103, Panamá 5, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, 522 510, India
| | - David A Donoso
- Departamento de Biología, Escuela Politécnica Nacional, Quito, Ecuador
- Centro de Investigación de la Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, EC170103, Quito, Ecuador
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, TF10 8NB, Shropshire, UK
| | - Daniel Souto-Vilarós
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44, Prague, Czech Republic
| | - Dina Y Soliman
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07, Uppsala, Sweden
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Greg P A Lamarre
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic
| | - Luis F De León
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103, Panamá 5, Panama
- Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA
| | - Thibaud Decaëns
- CEFE, University of Montpellier, CNRS, EPHE, IRD, University Paul Valéry, Montpellier 3, Montpellier, France
| | - José G Palacios-Vargas
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Gabriela Castaño-Meneses
- Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Universidad Nacional Autónoma de México, Campus Juriquilla, Juriquilla 76230, Querétaro, Mexico
| | - Rudolf H Scheffrahn
- Fort Lauderdale Research & Education Center, 3205 College Avenue, Davie, FL, 33314, USA
| | - Marleny Rivera
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Filonila Perez
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Ricardo Bobadilla
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Yacksecari Lopez
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | | | - Maira Montejo Cruz
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Angela Arango Galván
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Héctor Barrios
- Maestría de Entomología, Universidad de Panamá, 080814, Panama City, Republic of Panama
| |
Collapse
|
11
|
Marquina D, Roslin T, Łukasik P, Ronquist F. Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. MBMG 2022. [DOI: 10.3897/mbmg.6.78871] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DNA metabarcoding can accelerate research on insect diversity, as it is cheap and fast compared to manual sorting and identification. Most metabarcoding protocols require homogenisation of the sample, preventing further work on the specimens. Mild digestion of the tissue by incubation in a lysis buffer has been proposed as an alternative, and, although some mild lysis protocols have already been presented, they have so far not been evaluated against each other. Here, we analyse how two mild lysis buffers (one more aggressive, one gentler in terms of tissue degradation), two different incubation times, and two DNA purification methods (a manual precipitation and an automated protocol) affect the accuracy of retrieving the true composition of mock communities using two mitochondrial markers (COI and 16S). We found that protocol-specific variation in concentration and purity of the DNA extracts produced had little effect on the recovery of species. However, the two lysis treatments differed in quantification of species abundances. Digestion in the gentler buffer and for a shorter time yielded better representation of original sample composition. Digestion in a more aggressive buffer or longer incubation time yielded lower alpha diversity values and increased differences between metabarcoding results and the true species-abundance distribution. We conclude that the details of non-destructive protocols can have a significant effect on metabarcoding performance. A short and mild lysis treatment appears the best choice for recovering the true composition of the sample. This not only improves accuracy, but also comes with a faster processing time than the other treatments.
Collapse
|
12
|
Rahman MM, Burian A, Creedy TJ, Vogler AP. DNA
‐based assessment of environmental degradation in an unknown fauna: the freshwater macroinvertebrates of the
Indo‐Burmese
hotspot. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Md. Mizanur Rahman
- Department of Life Sciences, Natural History Museum London UK
- Department of Life Sciences, Silwood Park Campus Imperial College London Ascot UK
- Department of Zoology University of Dhaka Dhaka Bangladesh
| | - Alfred Burian
- Marine Ecology Department Lurio University Nampula Mozambique
- Department of Computational Landscape Ecology, UFZ–Helmholtz Centre for Environmental Research Leipzig Germany
| | - Thomas J. Creedy
- Department of Life Sciences, Natural History Museum London UK
- Department of Life Sciences, Silwood Park Campus Imperial College London Ascot UK
| | - Alfried P. Vogler
- Department of Life Sciences, Natural History Museum London UK
- Department of Life Sciences, Silwood Park Campus Imperial College London Ascot UK
| |
Collapse
|
13
|
Paula DP, Barros SKA, Pitta RM, Barreto MR, Togawa RC, Andow DA. Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators. Gigascience 2022; 11:6554098. [PMID: 35333301 PMCID: PMC8952265 DOI: 10.1093/gigascience/giac020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022] Open
Abstract
Background A central challenge of DNA gut content analysis is to identify prey in a highly degraded DNA community. In this study, we evaluated prey detection using metabarcoding and a method of mapping unassembled shotgun reads (Lazaro). Results In a mock prey community, metabarcoding did not detect any prey, probably owing to primer choice and/or preferential predator DNA amplification, while Lazaro detected prey with accuracy 43–71%. Gut content analysis of field-collected arthropod epigeal predators (3 ants, 1 dermapteran, and 1 carabid) from agricultural habitats in Brazil (27 samples, 46–273 individuals per sample) revealed that 64% of the prey species detections by either method were not confirmed by melting curve analysis and 87% of the true prey were detected in common. We hypothesized that Lazaro would detect fewer true- and false-positive and more false-negative prey with greater taxonomic resolution than metabarcoding but found that the methods were similar in sensitivity, specificity, false discovery rate, false omission rate, and accuracy. There was a positive correlation between the relative prey DNA concentration in the samples and the number of prey reads detected by Lazaro, while this was inconsistent for metabarcoding. Conclusions Metabarcoding and Lazaro had similar, but partially complementary, detection of prey in arthropod predator guts. However, while Lazaro was almost 2× more expensive, the number of reads was related to the amount of prey DNA, suggesting that Lazaro may provide quantitative prey information while metabarcoding did not.
Collapse
Affiliation(s)
- Débora Pires Paula
- Embrapa Genetic Resources and Biotechnology, Brasília-DF, 70770-917, Brazil
| | | | | | | | | | - David A Andow
- Department of Entomology, University of Minnesota, MN, 55108, St. Paul, USA
| |
Collapse
|
14
|
Koskinen JS, Abrego N, Vesterinen EJ, Schulz T, Roslin T, Nyman T. Imprints of latitude, host taxon, and decay stage on fungus‐associated arthropod communities. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Janne S. Koskinen
- Department of Environmental and Biological Sciences University of Eastern Finland Joensuu Finland
- Department of Agricultural Sciences University of Helsinki Finland
| | - Nerea Abrego
- Department of Agricultural Sciences University of Helsinki Finland
- Department of Biological and Environmental Science University of Jyväskylä Finland
| | | | - Torsti Schulz
- Organismal and Evolutionary Biology Research Programme University of Helsinki Finland
| | - Tomas Roslin
- Department of Agricultural Sciences University of Helsinki Finland
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region Norwegian Institute of Bioeconomy Research Svanvik Norway
| |
Collapse
|
15
|
Sire L, Yáñez PS, Wang C, Bézier A, Courtial B, Cours J, Fontaneto D, Larrieu L, Bouget C, Thorn S, Müller J, Yu DW, Monaghan MT, Herniou EA, Lopez-Vaamonde C. Climate-induced forest dieback drives compositional changes in insect communities that are more pronounced for rare species. Commun Biol 2022; 5:57. [PMID: 35042989 PMCID: PMC8766456 DOI: 10.1038/s42003-021-02968-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 12/07/2021] [Indexed: 12/26/2022] Open
Abstract
Species richness, abundance and biomass of insects have recently undergone marked declines in Europe. We metabarcoded 211 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging had an impact on ca. 3000 species of flying insects in silver fir Pyrenean forests. While forest dieback had no measurable impact on species richness, there were significant changes in community composition that were consistent with those observed during natural forest succession. Importantly, most observed changes were driven by rare species. Variation was explained primarily by canopy openness at the local scale, and the tree-related microhabitat diversity and deadwood amount at landscape scales. The levels of salvage logging in our study did not explain compositional changes. We conclude that forest dieback drives changes in species assemblages that mimic natural forest succession, and markedly increases the risk of catastrophic loss of rare species through homogenization of environmental conditions.
Collapse
Affiliation(s)
- Lucas Sire
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France.
| | - Paul Schmidt Yáñez
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
| | - Cai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
| | | | - Jérémy Cours
- INRAE 'Forest Ecosystems' Research Unit - Biodiversity team Domaine des Barres, F-45290, Nogent-sur-Vernisson, France
| | - Diego Fontaneto
- Water Research Institute, National Research Council of Italy, CNR-IRSA, Largo Tonolli 50, 28922, Verbania Pallanza, Italy
| | - Laurent Larrieu
- Université de Toulouse, INRAE, UMR DYNAFOR, Castanet-Tolosan, France
- CRPF Occitanie, Tarbes, France
| | - Christophe Bouget
- INRAE 'Forest Ecosystems' Research Unit - Biodiversity team Domaine des Barres, F-45290, Nogent-sur-Vernisson, France
| | - Simon Thorn
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstraße 5, 96181, Rauhenebrach, Germany
| | - Jörg Müller
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstraße 5, 96181, Rauhenebrach, Germany
- Bavarian Forest National Park, Freyunger Str. 2, 94481, Grafenau, Germany
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR47TJ, UK
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Königin-Luise-Straße. 1-3, 12489, Berlin, Germany
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
| | - Carlos Lopez-Vaamonde
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR 7261, CNRS-Université de Tours, Tours, France
- INRAE, Zoologie Forestière, F-45075, Orléans, France
| |
Collapse
|
16
|
Jiang M, Xu SF, Tang TS, Miao L, Luo BZ, Ni Y, Kong FD, Liu C. Development and evaluation of a meat mitochondrial metagenomic (3MG) method for composition determination of meat from fifteen mammalian and avian species. BMC Genomics 2022; 23:36. [PMID: 34996352 PMCID: PMC8742424 DOI: 10.1186/s12864-021-08263-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/17/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Bioassessment and biomonitoring of meat products are aimed at identifying and quantifying adulterants and contaminants, such as meat from unexpected sources and microbes. Several methods for determining the biological composition of mixed samples have been used, including metabarcoding, metagenomics and mitochondrial metagenomics. In this study, we aimed to develop a method based on next-generation DNA sequencing to estimate samples that might contain meat from 15 mammalian and avian species that are commonly related to meat bioassessment and biomonitoring. RESULTS In this project, we found the meat composition from 15 species could not be identified with the metabarcoding approach because of the lack of universal primers or insufficient discrimination power. Consequently, we developed and evaluated a meat mitochondrial metagenomics (3MG) method. The 3MG method has four steps: (1) extraction of sequencing reads from mitochondrial genomes (mitogenomes); (2) assembly of mitogenomes; (3) mapping of mitochondrial reads to the assembled mitogenomes; and (4) biomass estimation based on the number of uniquely mapped reads. The method was implemented in a python script called 3MG. The analysis of simulated datasets showed that the method can determine contaminant composition at a proportion of 2% and the relative error was < 5%. To evaluate the performance of 3MG, we constructed and analysed mixed samples derived from 15 animal species in equal mass. Then, we constructed and analysed mixed samples derived from two animal species (pork and chicken) in different ratios. DNAs were extracted and used in constructing 21 libraries for next-generation sequencing. The analysis of the 15 species mix with the method showed the successful identification of 12 of the 15 (80%) animal species tested. The analysis of the mixed samples of the two species revealed correlation coefficients of 0.98 for pork and 0.98 for chicken between the number of uniquely mapped reads and the mass proportion. CONCLUSION To the best of our knowledge, this study is the first to demonstrate the potential of the non-targeted 3MG method as a tool for accurately estimating biomass in meat mix samples. The method has potential broad applications in meat product safety.
Collapse
Affiliation(s)
- Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 100193 Beijing, PR China
| | - Shu-Fei Xu
- Technology Center of Xiamen Entry-exit Inspection and Quarantine Bureau, Xiamen, Fujian 361026 PR China
| | - Tai-Shan Tang
- Technology Center of Jiangsu Entry-exit Inspection and Quarantine Bureau, Nanjing, Jiangsu 210009 PR China
| | - Li Miao
- Technology Center of Henan Entry-exit Inspection and Quarantine Bureau, Zhengzhou, Henan 450003 PR China
| | - Bao-Zheng Luo
- Technology Center of Zhuhai Entry-exit Inspection and Quarantine Bureau, Zhuhai, Guangdong 519000 PR China
| | - Yang Ni
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002 PR China
| | - Fan-De Kong
- Technology Center of Xiamen Entry-exit Inspection and Quarantine Bureau, Xiamen, Fujian 361026 PR China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, 100193 Beijing, PR China
| |
Collapse
|
17
|
Huang J, Miao X, Wang Q, Menzel F, Tang P, Yang D, Wu H, Vogler AP. Metabarcoding reveals massive species diversity of Diptera in a subtropical ecosystem. Ecol Evol 2022; 12:e8535. [PMID: 35127039 PMCID: PMC8796913 DOI: 10.1002/ece3.8535] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/08/2021] [Accepted: 12/22/2021] [Indexed: 11/07/2022] Open
Abstract
Diptera is often considered to be the richest insect group due to its great species diversity and broad ecological versatility. However, data on dipteran diversity from subtropical ecosystems have hitherto been scarce, due to the lack of studies conducted at an appropriate large scale. We investigated the diversity and composition of Diptera communities on Tianmu Mountain, Zhejiang, China, using DNA metabarcoding technology, and evaluated their dynamic responses to the effects of slope aspect, season, and altitudinal zone. A total of 5,092 operational taxonomic units (OTUs) were discovered and tentatively assigned to 72 dipteran families, including 2 family records new for China and 30 family records new for the locality. Cecidomyiidae, Sciaridae, and Phoridae were the predominant families, representing 53.6% of total OTUs, while 52 families include >95% unidentified and presumed undescribed species. We found that the community structure of Diptera was significantly affected by aspect, seasonality (month) and elevation, with richer diversity harbored in north-facing than south-facing slopes, and seasonality a more profound driver of community structure and diversity than elevation. Overall, massive species diversity of Diptera communities was discovered in this subtropical ecosystem of east China. The huge diversity of potentially undescribed species only revealed by metabarcoding now requires more detailed taxonomic study, as a step toward an evolutionary integration that accumulates information on species' geographic ranges, ecological traits, functional roles, and species interactions, and thus places the local communities in the context of the growing knowledge base of global biodiversity and its response to environmental change.
Collapse
Affiliation(s)
- Junhao Huang
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Xiaoqian Miao
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Qingyun Wang
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Frank Menzel
- Senckenberg Deutsches Entomologisches InstitutMünchebergGermany
| | - Pu Tang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural EntomologyInstitute of Insect SciencesZhejiang UniversityHangzhouChina
| | - Ding Yang
- College of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Hong Wu
- Department of Forestry ProtectionSchool of Forestry and BiotechnologyZhejiang A&F UniversityHangzhouChina
| | - Alfried P. Vogler
- Department of Life SciencesNatural History MuseumLondonUK
- Department of Life SciencesImperial College LondonAscotUK
| |
Collapse
|
18
|
Bell KL, Petit RA, Cutler A, Dobbs EK, Macpherson JM, Read TD, Burgess KS, Brosi BJ. Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures. Ecol Evol 2021; 11:16082-16098. [PMID: 34824813 PMCID: PMC8601920 DOI: 10.1002/ece3.8281] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular identification of mixed-species pollen samples has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via amplicon sequencing, but whole-genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per sample and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each sample using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k-mer identification method with reference libraries constructed from full-genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 amplicon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but diverged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS-based pollen identification is the lack of representation of plant diversity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed-species pollen samples.
Collapse
Affiliation(s)
- Karen L Bell
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: School of Biological Sciences University of Western Australia Perth Australia
- Present address: CSIRO Land & Water and CSIRO Health & Biosecurity Floreat WA Australia
| | - Robert A Petit
- Division of Infectious Diseases Department of Medicine Emory University Atlanta Georgia USA
| | - Anya Cutler
- Department of Environmental Sciences Emory University Atlanta Georgia USA
| | - Emily K Dobbs
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: Department of Biology Northern Kentucky University Highland Heights Kentucky USA
| | - J Michael Macpherson
- Department of Biology Chapman University Orange California USA
- Present address: 23andMe Mountain View California USA
| | - Timothy D Read
- Division of Infectious Diseases Department of Medicine Emory University Atlanta Georgia USA
| | - Kevin S Burgess
- Department of Biology Columbus State University Columbus Georgia USA
| | - Berry J Brosi
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: Department of Biology University of Washington Seattle Washington USA
| |
Collapse
|
19
|
Roslin T, Somervuo P, Pentinsaari M, Hebert PDN, Agda J, Ahlroth P, Anttonen P, Aspi J, Blagoev G, Blanco S, Chan D, Clayhills T, deWaard J, deWaard S, Elliot T, Elo R, Haapala S, Helve E, Ilmonen J, Hirvonen P, Ho C, Itämies J, Ivanov V, Jakovlev J, Juslén A, Jussila R, Kahanpää J, Kaila L, Jari-PekkaKaitila, Kakko A, Kakko I, Karhu A, Karjalainen S, Kjaerandsen J, Koskinen J, Laasonen EM, Laasonen L, Laine E, Lampila P, Levesque-Beaudin V, Lu L, Lähteenaro M, Majuri P, Malmberg S, Manjunath R, Martikainen P, Mattila J, McKeown J, Metsälä P, Miklasevskaja M, Miller M, Miskie R, Muinonen A, Veli-MattiMukkala, Naik S, Nikolova N, Nupponen K, Ovaskainen O, Österblad I, Paasivirta L, Pajunen T, Parkko P, Paukkunen J, Penttinen R, Perez K, Pohjoismäki J, Prosser S, Raekunnas M, Rahulan M, Rannisto M, Ratnasingham S, Raukko P, Rinne A, Rintala T, Miranda Romo S, Salmela J, Salokannel J, Savolainen R, Schulman L, Sihvonen P, Soliman D, Sones J, Steinke C, Ståhls G, Tabell J, Tiusanen M, Várkonyi G, Vesterinen EJ, Viitanen E, Vikberg V, Viitasaari M, Vilen J, Warne C, Wei C, Winqvist K, Zakharov E, Mutanen M. A molecular-based identification resource for the arthropods of Finland. Mol Ecol Resour 2021; 22:803-822. [PMID: 34562055 DOI: 10.1111/1755-0998.13510] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.
Collapse
Affiliation(s)
- Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jireh Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Petri Ahlroth
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Perttu Anttonen
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Santiago Blanco
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dean Chan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Jeremy deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Stephanie deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Tyler Elliot
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Riikka Elo
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Jari Ilmonen
- Metsähallitus, Parks & Wildlife Finland, Vantaa, Finland
| | | | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Vladislav Ivanov
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | | | - Aino Juslén
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Jere Kahanpää
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Lauri Kaila
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Iiro Kakko
- Forssa Museum of Natural History, Forssa, Finland
| | | | | | - Jostein Kjaerandsen
- The Arctic University Museum of Norway, UiT -The Arctic University of Norway, Langnes, Tromsø, Norway
| | - Janne Koskinen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | | | | | | | | | | | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meri Lähteenaro
- Division of Systematics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Entomology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Meredith Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Nadia Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Timo Pajunen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Juho Paukkunen
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ritva Penttinen
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jaakko Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Sean Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Miduna Rahulan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meeri Rannisto
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | - Jukka Salmela
- Regional Museum of Lapland, Arktikum, Rovaniemi, Finland.,Arctic Centre, University of Lapland, Rovaniemi, Finland
| | | | - Riitta Savolainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Leif Schulman
- Finnish Environment Institute (SYKE), Helsinki, Finland.,Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Pasi Sihvonen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Dina Soliman
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Gunilla Ståhls
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Mikko Tiusanen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Gergely Várkonyi
- Biodiversity Centre, Finnish Environment Institute SYKE, Kuhmo, Finland
| | - Eero J Vesterinen
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Biology, University of Turku, Turku, Finland
| | | | | | | | | | - Connor Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Catherine Wei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Evgeny Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| |
Collapse
|
20
|
Kim JY, Yi M, Kim M, Lee S, Moon HS, Yong D, Yong T. Measuring the absolute abundance of the microbiome by adding yeast containing 16S rRNA gene from a hyperthermophile. Microbiologyopen 2021; 10:e1220. [PMID: 34459541 PMCID: PMC8302012 DOI: 10.1002/mbo3.1220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 06/24/2021] [Accepted: 06/26/2021] [Indexed: 11/09/2022] Open
Abstract
High-throughput sequencing (HTS) of 16S rRNA gene amplicons provides compositional information regarding the microbial community, but not the absolute abundance of the bacteria. We aimed to develop a standardized method for quantifying the absolute abundance of bacteria in microbiome studies. To demonstrate the utility of our approach, we quantified the number of bacteria from the compositional data of the fecal and cecal microbiomes. The 16S rRNA gene of a hyperthermophile, Thermus aquaticus, was cloned into Pichia pastoris (yeast) genome, and an equivalent amount of the yeast was added to the stool and cecal samples of mice before DNA extraction. 16S rRNA gene library construction and HTS were performed after DNA extraction. The absolute abundances of bacteria were calculated using T. aquaticus reads. The average relative abundances of T. aquaticus in the five stool and five cecal samples were 0.95% and 0.33%, respectively, indicating that the number of bacteria in a cecum sample is 2.9 times higher than that in a stool sample. The method proposed for quantifying the absolute abundance of the bacterial population in this study is expected to overcome the limitation of showing only compositional data in most microbiome studies.
Collapse
Affiliation(s)
- Ju Yeong Kim
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
- Brain Korea 21 PLUS Project for Medical ScienceYonsei University College of MedicineSeoulKorea
| | - Myung‐hee Yi
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
| | - Myungjun Kim
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
| | - Seogwon Lee
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
| | - Hye Su Moon
- Department of Laboratory Medicine and Research Institute of Bacterial ResistanceYonsei University College of MedicineSeoulKorea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial ResistanceYonsei University College of MedicineSeoulKorea
| | - Tai‐Soon Yong
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
| |
Collapse
|
21
|
Garrido-Sanz L, Senar MÀ, Piñol J. Relative species abundance estimation in artificial mixtures of insects using mito-metagenomics and a correction factor for the mitochondrial DNA copy number. Mol Ecol Resour 2021; 22:153-167. [PMID: 34251746 DOI: 10.1111/1755-0998.13464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 06/21/2021] [Accepted: 07/07/2021] [Indexed: 11/27/2022]
Abstract
Mito-metagenomics (MMG) is becoming an alternative to amplicon metabarcoding for the assessment of biodiversity in complex biological samples using high-throughput sequencing. Whereas MMG overcomes the biases introduced by the PCR step in the generation of amplicons, it is not yet a technique free of shortcomings. First, as the reads are obtained from shotgun sequencing, a very low proportion of reads map into the mitogenomes, so a high sequencing effort is needed. Second, as the number of mitogenomes per cell can vary among species, the relative species abundance (RSA) in a mixture could be wrongly estimated. Here, we challenge the MMG method to estimate the RSA using artificial libraries of 17 insect species whose complete genomes are available on public repositories. With fresh specimens of these species, we created single-species libraries to calibrate the bioinformatic pipeline and mixed-species libraries to estimate the RSA. Our results showed that the MMG approach confidently recovers the species list of the mixtures, even when they contain congeneric species. The method was also able to estimate the abundance of a species across different samples (within-species estimation) but failed to estimate the RSA within a single sample (across-species estimation) unless a correction factor accounting for the variable number of mitogenomes per cell was used. To estimate this correction factor, we used the proportion of reads mapping into mitogenomes in the single-species libraries and the lengths of the whole genomes and mitogenomes.
Collapse
Affiliation(s)
| | | | - Josep Piñol
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,CREAF, Cerdanyola del Vallès, Spain
| |
Collapse
|
22
|
Ferravante C, Memoli D, Palumbo D, Ciaramella P, Di Loria A, D'Agostino Y, Nassa G, Rizzo F, Tarallo R, Weisz A, Giurato G. HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis. BMC Bioinformatics 2021; 22:106. [PMID: 34225648 PMCID: PMC8256542 DOI: 10.1186/s12859-021-04004-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Background Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing not only the identification of known phyla and strains but also the discovery of novel ones. The large amount of metagenomic shotgun data produced by NGS require comprehensive and user-friendly pipelines for data analysis, that speed up the bioinformatics steps, relieving the users from the need to manually perform complex and time-consuming tasks. Results We describe here HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities), an exhaustive pipeline for metagenomics data analysis, comprising three independent analytical modules designed for an inclusive analysis of large NGS datasets. Conclusions HOME-BIO is a powerful and easy-to-use tool that can be run also by users with limited computational expertise. It allows in-depth analyses by removing low-complexity/ problematic reads, integrating the analytical steps that lead to a comprehensive taxonomy profile of each sample by querying different source databases, and it is customizable according to specific users’ needs.
Collapse
Affiliation(s)
- Carlo Ferravante
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy.,Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Naples, Italy.,Genomix4Life, via S. Allende 43/L, 84081, Baronissi, SA, Italy
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Domenico Palumbo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Paolo Ciaramella
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Naples, Italy
| | - Antonio Di Loria
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Naples, Italy
| | - Ylenia D'Agostino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy. .,CRGS - Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, SA, Italy.
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy.
| |
Collapse
|
23
|
Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
Collapse
Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
| |
Collapse
|
24
|
Yang C, Bohmann K, Wang X, Cai W, Wales N, Ding Z, Gopalakrishnan S, Yu DW. Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13602] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Kristine Bohmann
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Wang Cai
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Nathan Wales
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- Department of Archaeology University of York York UK
| | - Zhaoli Ding
- Biodiversity Genomics Center Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
- School of Biological Sciences University of East AngliaNorwich Research Park Norwich UK
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
| |
Collapse
|
25
|
Batovska J, Piper AM, Valenzuela I, Cunningham JP, Blacket MJ. Developing a non-destructive metabarcoding protocol for detection of pest insects in bulk trap catches. Sci Rep 2021; 11:7946. [PMID: 33846382 PMCID: PMC8041782 DOI: 10.1038/s41598-021-85855-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/02/2021] [Indexed: 01/04/2023] Open
Abstract
Metabarcoding has the potential to revolutionise insect surveillance by providing high-throughput and cost-effective species identification of all specimens within mixed trap catches. Nevertheless, incorporation of metabarcoding into insect diagnostic laboratories will first require the development and evaluation of protocols that adhere to the specialised regulatory requirements of invasive species surveillance. In this study, we develop a multi-locus non-destructive metabarcoding protocol that allows sensitive detection of agricultural pests, and subsequent confirmation using traditional diagnostic techniques. We validate this protocol for the detection of tomato potato psyllid (Bactericera cockerelli) and Russian wheat aphid (Diuraphis noxia) within mock communities and field survey traps. We find that metabarcoding can reliably detect target insects within mixed community samples, including specimens that morphological identification did not initially detect, but sensitivity appears inversely related to community size and is impacted by primer biases, target loci, and sample indexing strategy. While our multi-locus approach allowed independent validation of target detection, lack of reference sequences for 18S and 12S restricted its usefulness for estimating diversity in field samples. The non-destructive DNA extraction proved invaluable for resolving inconsistencies between morphological and metabarcoding identification results, and post-extraction specimens were suitable for both morphological re-examination and DNA re-extraction for confirmatory barcoding.
Collapse
Affiliation(s)
- Jana Batovska
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Alexander M Piper
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Isabel Valenzuela
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - John Paul Cunningham
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Mark J Blacket
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| |
Collapse
|
26
|
Marquina D, Buczek M, Ronquist F, Łukasik P. The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies. PeerJ 2021; 9:e10799. [PMID: 33614282 PMCID: PMC7883690 DOI: 10.7717/peerj.10799] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/29/2020] [Indexed: 12/20/2022] Open
Abstract
Traditionally, insects collected for scientific purposes have been dried and pinned, or preserved in 70% ethanol. Both methods preserve taxonomically informative exoskeletal structures well but are suboptimal for preserving DNA for molecular biology. Highly concentrated ethanol (95–100%), preferred as a DNA preservative, has generally been assumed to make specimens brittle and prone to breaking. However, systematic studies on the correlation between ethanol concentration and specimen preservation are lacking. Here, we tested how preservative ethanol concentration in combination with different sample handling regimes affect the integrity of seven insect species representing four orders, and differing substantially in the level of sclerotization. After preservation and treatments (various levels of disturbance), we counted the number of appendages (legs, wings, antennae, or heads) that each specimen had lost. Additionally, we assessed the preservation of DNA after long-term storage by comparing the ratio of PCR amplicon copy numbers to an added artificial standard. We found that high ethanol concentrations indeed induce brittleness in insects. However, the magnitude and nature of the effect varied strikingly among species. In general, ethanol concentrations at or above 90% made the insects more brittle, but for species with robust, thicker exoskeletons, this did not translate to an increased loss of appendages. Neither freezing the samples nor drying the insects after immersion in ethanol had a negative effect on the retention of appendages. However, the morphology of the insects was severely damaged if they were allowed to dry. We also found that DNA preserves less well at lower ethanol concentrations when stored at room temperature for an extended period. However, the magnitude of the effect varies among species; the concentrations at which the number of COI amplicon copies relative to the standard was significantly decreased compared to 95% ethanol ranged from 90% to as low as 50%. While higher ethanol concentrations positively affect long-term DNA preservation, there is a clear trade-off between preserving insects for morphological examination and genetic analysis. The optimal ethanol concentration for the latter is detrimental for the former, and vice versa. These trade-offs need to be considered in large insect biodiversity surveys and other projects aiming to combine molecular work with traditional morphology-based characterization of collected specimens.
Collapse
Affiliation(s)
- Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Piotr Łukasik
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| |
Collapse
|
27
|
Høye TT, Loboda S, Koltz AM, Gillespie MAK, Bowden JJ, Schmidt NM. Nonlinear trends in abundance and diversity and complex responses to climate change in Arctic arthropods. Proc Natl Acad Sci U S A 2021; 118:e2002557117. [PMID: 33431570 PMCID: PMC7812779 DOI: 10.1073/pnas.2002557117] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Time series data on arthropod populations are critical for understanding the magnitude, direction, and drivers of change. However, most arthropod monitoring programs are short-lived and restricted in taxonomic resolution. Monitoring data from the Arctic are especially underrepresented, yet critical to uncovering and understanding some of the earliest biological responses to rapid environmental change. Clear imprints of climate on the behavior and life history of some Arctic arthropods have been demonstrated, but a synthesis of population-level abundance changes across taxa is lacking. We utilized 24 y of abundance data from Zackenberg in High-Arctic Greenland to assess trends in abundance and diversity and identify potential climatic drivers of abundance changes. Unlike findings from temperate systems, we found a nonlinear pattern, with total arthropod abundance gradually declining during 1996 to 2014, followed by a sharp increase. Family-level diversity showed the opposite pattern, suggesting increasing dominance of a small number of taxa. Total abundance masked more complicated trajectories of family-level abundance, which also frequently varied among habitats. Contrary to expectation in this extreme polar environment, winter and fall conditions and positive density-dependent feedbacks were more common determinants of arthropod dynamics than summer temperature. Together, these data highlight the complexity of characterizing climate change responses even in relatively simple Arctic food webs. Our results underscore the need for data reporting beyond overall trends in biomass or abundance and for including basic research on life history and ecology to achieve a more nuanced understanding of the sensitivity of Arctic and other arthropods to global changes.
Collapse
Affiliation(s)
- Toke T Høye
- Arctic Research Centre, Aarhus University, DK-8410 Rønde, Denmark;
- Department of Bioscience, Aarhus University, DK-8410 Rønde, Denmark
| | - Sarah Loboda
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Amanda M Koltz
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
- The Arctic Institute, Washington, DC 20009
| | - Mark A K Gillespie
- Department of Environmental Sciences, Western Norway University of Applied Sciences, 6851 Sogndal, Norway
| | - Joseph J Bowden
- Atlantic Forestry Centre, Canadian Forest Service, Natural Resources Canada, Corner Brook, NL A2H 5G4, Canada
| | - Niels M Schmidt
- Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark
- Department of Bioscience, Aarhus University, DK-4000 Roskilde, Denmark
| |
Collapse
|
28
|
Bailet B, Apothéloz-Perret-Gentil L, Baričević A, Chonova T, Franc A, Frigerio JM, Kelly M, Mora D, Pfannkuchen M, Proft S, Ramon M, Vasselon V, Zimmermann J, Kahlert M. Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization. Sci Total Environ 2020; 745:140948. [PMID: 32736102 DOI: 10.1016/j.scitotenv.2020.140948] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 06/11/2023]
Abstract
Ecological assessment of lakes and rivers using benthic diatom assemblages currently requires considerable taxonomic expertise to identify species using light microscopy. This traditional approach is also time-consuming. Diatom metabarcoding is a promising alternative and there is increasing interest in using this approach for routine assessment. However, until now, analysis protocols for diatom metabarcoding have been developed and optimised by research groups working in isolation. The diversity of existing bioinformatics methods highlights the need for an assessment of the performance and comparability of results of different methods. The aim of this study was to test the correspondence of outputs from six bioinformatics pipelines currently in use for diatom metabarcoding in different European countries. Raw sequence data from 29 biofilm samples were treated by each of the bioinformatics pipelines, five of them using the same curated reference database. The outputs of the pipelines were compared in terms of sequence unit assemblages, taxonomic assignment, biotic index score and ecological assessment outcomes. The three last components were also compared to outputs from traditional light microscopy, which is currently accepted for ecological assessment of phytobenthos, as required by the Water Framework Directive. We also tested the performance of the pipelines on the two DNA markers (rbcL and 18S-V4) that are currently used by the working groups participating in this study. The sequence unit assemblages produced by different pipelines showed significant differences in terms of assigned and unassigned read numbers and sequence unit numbers. When comparing the taxonomic assignments at genus and species level, correspondence of the taxonomic assemblages between pipelines was weak. Most discrepancies were linked to differential detection or quantification of taxa, despite the use of the same reference database. Subsequent calculation of biotic index scores also showed significant differences between approaches, which were reflected in the final ecological assessment. Use of the rbcL marker always resulted in better correlation among molecular datasets and also in results closer to these generated using traditional microscopy. This study shows that decisions made in pipeline design have implications for the dataset's structure and the taxonomic assemblage, which in turn may affect biotic index calculation and ecological assessment. There is a need to define best-practice bioinformatics parameters in order to ensure the best representation of diatom assemblages. Only the use of similar parameters will ensure the compatibility of data from different working groups. The future of diatom metabarcoding for ecological assessment may also lie in the development of new metrics using, for example, presence/absence instead of relative abundance data.
Collapse
Affiliation(s)
- Bonnie Bailet
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE - 750 07 Uppsala, Sweden.
| | | | - Ana Baričević
- Center for Marine Research, Ruđer Bosˇković Institute, Rovinj, Croatia.
| | - Teofana Chonova
- Research Department for Limnology, Mondsee, Faculty of Biology, University of Innsbruck, Mondsee, Austria; CARRTEL, French National Institute for Agricultural Research (INRA), University of Savoie Mont Blanc, 75 bis avenue de Corzent, 74200 Thonon-les-Bains, France.
| | - Alain Franc
- BioGeCo, French National Institute for Agricultural Research (INRA), 69 route d'Arcachon, 33610 Cesta, France.
| | - Jean-Marc Frigerio
- BioGeCo, French National Institute for Agricultural Research (INRA), 69 route d'Arcachon, 33610 Cesta, France.
| | - Martyn Kelly
- Bowburn Consultancy, 11 Monteigne Drive, Bowburn, Durham DH6 5QB, UK; School of Geography, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Demetrio Mora
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany.
| | | | - Sebastian Proft
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany
| | | | - Valentin Vasselon
- AFB, Pôle R&D "ECLA", INRA, UMR CARRTEL, 75bis av. de Corzent - CS 50511, FR-74200 Thonon-les-Bains, France
| | - Jonas Zimmermann
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany.
| | - Maria Kahlert
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE - 750 07 Uppsala, Sweden.
| |
Collapse
|
29
|
Macher JN, Drakou K, Papatheodoulou A, Hoorn BVD, Vasquez M. The mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus. MBMG 2020. [DOI: 10.3897/mbmg.4.58259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aquatic macroinvertebrates are often identified, based on morphology, but molecular approaches like DNA barcoding, metabarcoding and metagenomics are increasingly used for species identification. These approaches require the availability of DNA references deposited in public databases. Here we report the mitochondrial genomes of 11 aquatic macroinvertebrate species from Cyprus, a European Union island country in the Mediterranean. Only three species could be provisionally assigned to a binomial species name, highlighting the current lack of molecular references for aquatic macroinvertebrates from Cyprus.
Graphical Abstract
Collapse
|
30
|
Harrison JG, John Calder W, Shuman B, Alex Buerkle C. The quest for absolute abundance: The use of internal standards for DNA-based community ecology. Mol Ecol Resour 2020; 21:30-43. [PMID: 32889760 DOI: 10.1111/1755-0998.13247] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/10/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022]
Abstract
To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional data are inherently constrained and difficult to interpret. The incorporation of internal standards (ISDs; colloquially referred to as 'spike-ins') into DNA pools can ameliorate the problems posed by relative abundance data and allow absolute abundances to be approximated. Unfortunately, many laboratory and sampling biases cause ISDs to underperform or fail. Here, we discuss how careful deployment of ISDs can avoid these complications and be an integral component of well-designed studies seeking to characterize ecological assemblages via sequencing of DNA.
Collapse
|
31
|
Uiterwaal SF, DeLong JP. Using patterns in prey DNA digestion rates to quantify predator diets. Mol Ecol Resour 2020; 20:1723-1732. [PMID: 32688451 DOI: 10.1111/1755-0998.13231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/01/2020] [Accepted: 07/10/2020] [Indexed: 11/26/2022]
Abstract
Dietary metabarcoding-the process of taxonomic identification of food species from DNA in consumer guts or faeces-has been rapidly adopted by ecologists to gain insights into biocontrol, invasive species and the structure of food webs. However, an outstanding issue with metabarcoding is the semi-quantitative nature of the data it provides: because metabarcoding is likely to produce false negatives for some prey more often than for other prey, we cannot infer relative frequencies of prey in the diet. To correct for this, we can adjust detected prey frequencies using DNA detectability half-lives unique to each predator-prey combination. Because the feeding experiments required to deduce these half-lives are time- and resource-intensive, our ability to weight the frequency of observations using their detectability has thus far been limited to systems with just a few prey. Here, we present a meta-analysis of 24 spider prey DNA half-lives and show that these half-lives are predictable given predator and prey mass, predator family, digestion temperature and DNA amplicon length. We further provide a new technique for weighting observations with half-lives, which allows not just for the ranking of prey in the diet, but reveals the proportion of the diet each prey comprises. Lastly, we apply this method to published dietary metabarcoding data to calculate half-lives and proportion of the predator's diet for 35 prey families, demonstrating that this technique can generate improved understanding of diets in real, diverse systems.
Collapse
Affiliation(s)
- Stella F Uiterwaal
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - John P DeLong
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| |
Collapse
|
32
|
Giebner H, Langen K, Bourlat SJ, Kukowka S, Mayer C, Astrin JJ, Misof B, Fonseca VG. Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes. Mol Ecol Resour 2020; 20:1333-1345. [PMID: 32462738 DOI: 10.1111/1755-0998.13201] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/20/2020] [Accepted: 05/15/2020] [Indexed: 12/25/2022]
Abstract
Environmental DNA studies targeting multiple taxa using metabarcoding provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are the presence of primer bias and difficulty in identifying rare species. We tested a DNA sequence-capture method in parallel with the metabarcoding approach to reveal possible advantages of one method over the other. Both approaches were performed using the same eDNA samples and the same 18S and COI regions, followed by high throughput sequencing. Metabarcoded eDNA libraries were PCR amplified with one primer pair from 18S and COI genes. DNA sequence-capture libraries were enriched with 3,639 baits targeting the same gene regions. We tested amplicon sequence variants (ASVs) and operational taxonomic units (OTUs) in silico approaches for both markers and methods, using for this purpose the metabarcoding data set. ASVs methods uncovered more species for the COI gene, whereas the opposite occurred for the 18S gene, suggesting that clustering reads into OTUs could bias diversity richness especially using 18S with relaxed thresholds. Additionally, metabarcoding and DNA sequence-capture recovered 80%-90% of the control sample species. DNA sequence-capture was 8x more expensive, nonetheless it identified 1.5x more species for COI and 13x more genera for 18S than metabarcoding. Both approaches offer reliable results, sharing ca. 40% species and 72% families and retrieve more taxa when nuclear and mitochondrial markers are combined. eDNA metabarcoding is quite well established and low-cost, whereas DNA-sequence capture for biodiversity assessment is still in its infancy, is more time-consuming but provides more taxonomic assignments.
Collapse
Affiliation(s)
- Hendrik Giebner
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Kathrin Langen
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Sarah J Bourlat
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Sandra Kukowka
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Christoph Mayer
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Jonas J Astrin
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany
| | - Vera G Fonseca
- Zoological Research Museum Alexander Koenig (ZFMK), Leibniz-Institute for Animal Biodiversity, Bonn, Germany.,Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK
| |
Collapse
|
33
|
Bell KL, Batchelor KL, Bradford M, McKeown A, Macdonald SL, Westcott D. Optimisation of a pollen DNA metabarcoding method for diet analysis of flying-foxes (Pteropus spp.). AUST J ZOOL 2020. [DOI: 10.1071/zo20085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Determining the diet of flying-foxes can increase understanding of how they function as pollinators and seed dispersers, as well as managing any negative impacts of large roosts. Traditional methods for diet analysis are time consuming, and not feasible to conduct for hundreds of animals. In this study, we optimised a method for diet analysis, based on DNA metabarcoding of environmental DNA (eDNA) from pollen and other plant parts in the faeces. We found that existing eDNA metabarcoding protocols are suitable, with the most useful results being obtained using a commercial food DNA extraction kit, and sequencing 350–450 base pairs of a DNA barcode from the internally transcribed spacer region (ITS2), with ~550 base pairs of the chloroplast rubisco large subunit (rbcL) as a secondary DNA barcode. A list of forage plants was generated for the little red flying-fox (Pteropus scapulatus), the black flying-fox (Pteropus alecto) and the spectacled flying-fox (Pteropus conspicillatus) from our collection sites across Queensland. The diets were determined to comprise predominantly Myrtaceae species, particularly those in the genera Eucalyptus, Melaleuca and Corymbia. With more plant genomes becoming publicly available in the future, there are likely to be further applications of eDNA methods in understanding the role of flying-foxes as pollinators and seed dispersers.
Collapse
|
34
|
Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 2019; 8:giz092. [PMID: 31363753 PMCID: PMC6667344 DOI: 10.1093/gigascience/giz092] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.
Collapse
Affiliation(s)
- Alexander M Piper
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Jana Batovska
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - John Weiss
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - John Paul Cunningham
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| |
Collapse
|